How can i keep deformed skinned mesh and rigged bones after scaling them?
Pose your model as wanted, select your mesh, in the properties panel - object mode  - apply the armature modifier, select the armature in pose mode, select all bones, Ctrl+A
 "Apply pose as rest pose", then select the mesh and readd an armature modifier, choose your rig as "object".

Be aware that the new rig will not execute old animations properly.